SMTL ID : 5xmp.2 (1 other biounit)

Plasmodium vivax SHMT(C346A) bound with PLP-glycine and MF057

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)

PLG.1: 21 residues within 4Å: Chain A: S.34, S.100, G.101, S.102, N.105, H.129, Y.182, T.183, D.208, S.210, H.211, T.234, H.236, K.237, R.371 Chain B: Y.54, E.56, Y.64, G.271, G.272 Ligands: 8A3.2 20 PLIP interactions: 4 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:Y.54, B:Y.64, B:G.271, B:G.272, A:S.34, A:G.101, A:S.102, A:N.105, A:H.129, A:S.210 Hydrophobic interactions: A:T.183 Water bridges: A:S.100, A:S.100, A:S.100, A:S.100 Salt bridges: A:H.211, A:H.236, A:K.237, A:R.371 pi-Stacking: A:H.129 PLG.4: 21 residues within 4Å: Chain A: Y.54, E.56, Y.64, G.271, G.272 Chain B: S.34, S.100, G.101, S.102, N.105, H.129, Y.182, T.183, D.208, S.210, H.211, T.234, H.236, K.237, R.371 Ligands: 8A3.5 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.183 Hydrogen bonds: B:S.34, B:G.101, B:S.102, B:N.105, B:H.129, B:S.210, A:G.271, A:G.272 Water bridges: B:S.100, B:S.100, B:S.100, B:S.100 Salt bridges: B:H.211, B:H.236, B:K.237, B:R.371 pi-Stacking: B:H.129

2 x 8A3: 4-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-(trifluoromethyl)phenyl]-~{N}-methyl-~{N}-[2,2,2-tris(fluoranyl)ethyl]benzenesulfonamide(Non-covalent)

8A3.2: 19 residues within 4Å: Chain A: L.124, G.127, G.128, H.129, L.130, V.141, T.183, N.354, K.355, N.356, T.357, A.364, P.367, R.371 Chain B: E.56, Y.63, Y.64, P.267 Ligands: PLG.1 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.124, B:Y.63, B:Y.64 Hydrogen bonds: A:G.127, A:T.183, A:T.357, B:E.56, B:Y.63 Halogen bonds: A:K.355, A:A.364 8A3.5: 19 residues within 4Å: Chain A: E.56, Y.63, Y.64, P.267 Chain B: L.124, G.127, G.128, H.129, L.130, V.141, T.183, N.354, K.355, N.356, T.357, A.364, P.367, R.371 Ligands: PLG.4 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.124, A:Y.63, A:Y.64 Hydrogen bonds: B:G.127, B:T.357, A:E.56 Halogen bonds: B:K.355, B:A.364

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: N.276, K.277 Chain B: N.276, K.277 Ligands: CL.6 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: N.276, K.277 Chain B: N.276, K.277 Ligands: CL.3 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schwertz, G. et al., Conformational Aspects in the Design of Inhibitors for Serine Hydroxymethyltransferase (SHMT): Biphenyl, Aryl Sulfonamide, and Aryl Sulfone Motifs. Chemistry (2017)

Release Date

2017-11-29

Peptides

Serine hydroxymethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Serine hydroxymethyltransferase

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